Identify the cluster 14(0.9) from harmony integration in normal CD4 Tcells

1. load libraries

2. Load Seurat Object

#Load Seurat Object merged from cell lines and a control after filtration
load("CD4Tcells_harmony_integrated_0.5_theta_patientorigin_orig_ident.Robj")

3. Identify the cluster

FeaturePlot(All_samples_Merged, features = c("CLEC4E", "IL1B", "LILRA5"))

VlnPlot(All_samples_Merged, features = c("CLEC4E", "IL1B", "LILRA5", "FCN1", "S100A8"), group.by = "cell_line")


VlnPlot(All_samples_Merged, features = c("CLEC4E", "IL1B", "LILRA5", "FCN1", "S100A8"), group.by = "harmony_res_0.9")

# List of genes you want to check
genes_of_interest <- c("CLEC4E", "IL1B", "LILRA5", "KCNE3", "PID1", "MPEG1", 
                       "FCN1", "S100A8", "OLR1", "G0S2", "ASGR2", "SPINK1", 
                       "SEMA6B", "HCK", "LYZ", "EREG", "SERPINB2", "LGALS2", 
                       "LINC01283", "CXCL1")

VlnPlot(All_samples_Merged, 
        features = genes_of_interest, # First 8 markers
        stack = TRUE,
        flip = TRUE) +
        ggtitle("CD4 T Cell Marker Distribution Across Clusters")